Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcaaaaaatactgagtgctagcattatgttctttatgtgcccagaagttactactagatcacaacactcttgattattattattaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os04g43750.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G089767_T01 (Zea mays), 3'ss of exon 2
gtaagttcaaaaaatactgagtgctagcatt--atgttcttta--tgtgcccag----aagttactac-taga-tcacaacactcttgattattattat--taatatt-tattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTAAT
||||| || || | | || ||| | | | || | || |||| | | ||| || | ||| || | | | || | || | | ||| || ||||||||||| || |||||||||||| |||||||||| |||||||| |||||||| ||||| |||||||||||||| ||| | |||||| | |||||| |||
gtaagctctgaagaaaaaccacaataatattcaaagctattagcctatgaccagtcctgattggttacataaactcataagaaattaaaacataacaatcctgacattacttttcagTGGATGCTTCAAATTCCTGGTGCATCAAGTTACATTGGTTGCATCGGGAAGGATAAGTTTGGTGAGGAGATGAAAAAAAATGCACAAGCTGCTGGTATTA--
upper sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G36630.1 (Glycine max), 3'ss of exon 4
gtaagttcaaaaaatactgagtgctagcattat--gttctttatg-tgcccagaagttactactagatcacaacactcttgattattatt-attaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTAAT
| || | || | || ||| | | | | ||| || || ||| | || ||| || | | | || ||| ||||||||||||| |||||||||||||||||||||||||| |||| || ||||| ||||| || || ||||||||||| || || | |||||||| |
----------------gtatgtatctaccttgttagtgcttagtaatactctgaatcta-tattagctttggtcaaagcaatttaccctttacttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAAGCTTGCTGGTGTAA--
upper sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G33910.3 (Glycine max), 3'ss of exon 1
gtaagttcaaaaaatactgagtgctagcat-tatgttctttatg-tgcccagaagttactactagatcacaacactcttgattattatt-attaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTAAT
|||| ||| |||| || || || | | | | ||| | || ||| | || ||| || | | | || ||| ||||||||||||| |||||||||||||||||||||||||| |||| || ||||| ||||| || || ||||||||||| || || |||||||| |
----aatcaaggttgctcaagtat--gcatctaccttgttagtaatactctgaatctg-tagtagctttggtcaaagcaatttaccctttacttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAGGCTTGCTGGTGTAA--
upper sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G33910.2 (Glycine max), 3'ss of exon 3
gtaagttcaaaaaatactgagtgctagcattatgttctttatgtgcccagaagttacta--ctagatcacaacactcttgattattattattaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTAAT
| ||| | |||| | || | | || || | | ||| | || | | | ||| | | || ||| ||||||||||||| |||||||||||||||||||||||||| |||| || ||||| ||||| || || ||||||||||| || || |||||||| |
------------------gtatgcatctaccttgttagtaatactctgaatctgtagtagctttggtcaaagcaatttaccct----ttacttttgcttcttgtagTGGATGCTCCAAGTTCCTGGTGCAACAAGTTACATGGGTGGCATAGGAAAGGATAAGTTTGGGGAAGAGATGAAGAAGAACTCAAGGCTTGCTGGTGTAA--
upper sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G06580.1 (Glycine max), 3'ss of exon 4
gtaagttcaaaaaatactgagtgctagcattatgttctttatgt--gcccagaagttactac-tagatcacaacactcttgattattattattaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAA-AGACGCACAAACCGCTGGTGTTAAT
| ||| | | || | || | | | ||| | | | || | ||| | || | | || ||||||||||| || || ||||| |||||||| || |||||||| || |||||||| || || |||||||||||||| | | | ||| | |||||| |
----------------------gtatgcactttcttttataagctgagtctggagtagttgtgttacttgtgtagctaatcatttgtcttcacttcactcataacagTGGATGCTTCAAGCACCAGGTGCCACAAGTTATATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TAGATGGTGTAA--
upper sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 4
gtaagttcaaaaaatactgagtgctagcattatgttctttatgtgcccagaagttactactagatcacaacactcttgattattattattaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAA-AGACGCACAAACCGCTGGTGTTAAT
|| | | |||||| | | | ||| | | | || |||||| || | || || |||||||||| || || ||||| ||||||||||| |||||||| || |||||||| || || |||||||||||||| | | | ||| | |||||| |
-------------gtatgcactttcttttatatgttgtaagctgagtctggagtagttgt--gttacttgtgtagttaattatttgccttcac-ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TTGATGGTGTAA--
upper sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv13s0019g04470.t01 (Vitis vinifera), 3'ss of exon 4
gtaagttcaaaaaatactgagtgctagcattatgttctttatgtgcccagaagttactactagatcacaa-cactcttgattattattattaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTAAT
|| || |||||| | | | | ||| || ||| | | || | || || || | | || | | | | |||||||||||||| || || ||||| |||||||| || ||||| |||||||| ||||||||||| || ||||| ||||||||| || || || ||||||||||
----gtacataaaatatttactattgagcttagctttccgctgtattt---tctaattaagaaattgcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA--
upper sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv13s0019g04480.t01 (Vitis vinifera), 3'ss of exon 4
gtaagttcaaaaaatactgagtgctagcattatgttctttatgtgcccagaagttactactagatcacaacactcttgattattattattaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTAAT
|| || |||||| | | | | ||| || | ||| | ||| | | | || | | || | | | | |||||||||||||| || || ||||| |||||||| || ||||| |||||||| ||||||||||| || ||||| ||||||||| || || || ||||||||||
----gtacataaaatatttactattgagcttagctttcatctgtattttctaattaaga--aatttcattcattttctcaccttgccttgtgtgtgttttgcagTGGATGCTTCAAATCCCTGGAGCAACAAGCTATATGGGATGCATTGGAAAGGACAAGTTTGGGGAGGAAATGAAGAAAAACTCAAAACTTGCTGGTGTTA-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatcacaacactcttgattattattattaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTAAT
tattaat putative branch site (score: 2)
acaacactcttgatta TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcaaaaaatactgagtgctagcattatgttctttatgtgcccagaagttactactagatcacaacactcttgattattattattaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAAAGACGCACAAACCGCTGGTGTTAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA